Add min "thickness" check in CifParser to filter invalid structure …

…which leads to infinite loop (#4133)

* add min_vol check

* increase min_vol to 1

* round volume to 4 digits

* add test

* use min thickness for robustness

* compress test file

* lower the threshold even further

* update comment

src/pymatgen/io/cif.py

@@ -969,8 +969,22 @@ def _get_structure(
         primitive: bool,
         symmetrized: bool,
         check_occu: bool = False,
+        min_thickness: float = 0.01,
     ) -> Structure | None:
-        """Generate structure from part of the CIF."""
+        """Generate structure from part of the CIF.
+
+        Args:
+            data (CifBlock): The data block to parse.
+            primitive (bool): Whether to return primitive unit cells.
+            symmetrized (bool): Whether to return SymmetrizedStructure.
+            check_occu (bool): Whether to check site for unphysical occupancy > 1.
+            min_thickness (float): Minimum thickness in Angstrom to consider structure as valid.
+                This is added to guard against unphysical small/thin structure,
+                which could result in infinite loop for searching near neighbours.
+
+        Returns:
+            Structure or None if not found.
+        """
 
         def get_num_implicit_hydrogens(symbol: str) -> int:
             """Get number of implicit hydrogens."""
@@ -992,6 +1006,12 @@ def get_matching_coord(
 
         lattice = self.get_lattice(data)
 
+        # Check minimal lattice thickness
+        if lattice is not None:
+            thickness = [lattice.d_hkl((1, 0, 0)), lattice.d_hkl((0, 1, 0)), lattice.d_hkl((0, 0, 1))]
+            if any(t < min_thickness for t in thickness):
+                raise ValueError(f"{thickness=} Å below threshold, double check your structure.")
+
         # If magCIF, get magnetic symmetry moments and magmoms
         # else standard CIF, and use empty magmom dict
         if self.feature_flags["magcif_incommensurate"]:

tests/io/test_cif.py

@@ -219,6 +219,18 @@ def test_cif_parser(self):
         assert len(parser.parse_structures(primitive=False)[0]) == 2
         assert not parser.has_errors
 
+    def test_parse_bad_superflat(self):
+        """
+        Test unphysically "flat" structure with volume near zero,
+        which would originally lead to infinite loop (PR4133).
+        """
+        parser = CifParser(f"{TEST_FILES_DIR}/cif/bad_superflat_inf_loop.cif.gz")
+        with (
+            pytest.raises(ValueError, match="Invalid CIF file with no structures"),
+            pytest.warns(UserWarning, match="Å below threshold, double check your structure."),
+        ):
+            parser.parse_structures()
+
     def test_get_symmetrized_structure(self):
         parser = CifParser(f"{TEST_FILES_DIR}/cif/Li2O.cif")
         sym_structure = parser.parse_structures(primitive=False, symmetrized=True)[0]